@genome-spy/app 0.57.0 → 0.58.0

package/dist/{index-Bg62fPK7.js → index-DwLfOHEk.js}

@@ -1,9 +1,9 @@
-import { L as j, u as R, a as V } from "./long-DM5IWGqg.js";
-import { b as I } from "./index-DluFz_0j.js";
+import { L as Y, u as P, a as Q } from "./long-BviWyoZx.js";
+import { b as y } from "./index-BftNdA0O.js";
 import { L as C } from "./__vite-browser-external-C--ziKoh.js";
-import { R as k } from "./remoteFile-DwSeXAZ0.js";
-import { A as Q, L as Y } from "./index-C159nEYc.js";
-class D {
+import { R as L } from "./remoteFile-BuaqFGWk.js";
+import { A as W, L as X } from "./index-CCJIjehY.js";
+class O {
   constructor(e, t) {
     this.blockPosition = e, this.dataPosition = t;
   }
@@ -25,9 +25,9 @@ class D {
 function E(o, e = 0, t = !1) {
   if (t)
     throw new Error("big-endian virtual file offsets not implemented");
-  return new D(o[e + 7] * 1099511627776 + o[e + 6] * 4294967296 + o[e + 5] * 16777216 + o[e + 4] * 65536 + o[e + 3] * 256 + o[e + 2], o[e + 1] << 8 | o[e]);
+  return new O(o[e + 7] * 1099511627776 + o[e + 6] * 4294967296 + o[e + 5] * 16777216 + o[e + 4] * 65536 + o[e + 3] * 256 + o[e + 2], o[e + 1] << 8 | o[e]);
 }
-class $ {
+class F {
   constructor(e, t, n, r) {
     this.minv = e, this.maxv = t, this.bin = n, this._fetchedSize = r;
   }
@@ -44,15 +44,10 @@ class $ {
     return this._fetchedSize !== void 0 ? this._fetchedSize : this.maxv.blockPosition + 65536 - this.minv.blockPosition;
   }
 }
-function W(o) {
+function J(o) {
   return new Promise((e) => setTimeout(e, o));
 }
-function X(o) {
-  if (o.greaterThan(Number.MAX_SAFE_INTEGER) || o.lessThan(Number.MIN_SAFE_INTEGER))
-    throw new Error("integer overflow");
-  return o.toNumber();
-}
-function J(o) {
+function K(o) {
   if (o && o.aborted)
     if (typeof DOMException > "u") {
       const e = new Error("aborted");
@@ -60,13 +55,13 @@ function J(o) {
     } else
       throw new DOMException("aborted", "AbortError");
 }
-function K(o, e) {
+function Z(o, e) {
   return e.minv.blockPosition - o.maxv.blockPosition < 65e3 && e.maxv.blockPosition - o.minv.blockPosition < 5e6;
 }
-function Z(o = {}) {
+function ee(o = {}) {
   return "aborted" in o ? { signal: o } : o;
 }
-function U(o, e) {
+function z(o, e) {
   const t = [];
   let n;
   if (o.length === 0)
@@ -76,16 +71,18 @@ function U(o, e) {
     return i === 0 ? r.minv.dataPosition - s.minv.dataPosition : i;
   });
   for (const r of o)
-    (!e || r.maxv.compareTo(e) > 0) && (n === void 0 ? (t.push(r), n = r) : K(n, r) ? r.maxv.compareTo(n.maxv) > 0 && (n.maxv = r.maxv) : (t.push(r), n = r));
+    (!e || r.maxv.compareTo(e) > 0) && (n === void 0 ? (t.push(r), n = r) : Z(n, r) ? r.maxv.compareTo(n.maxv) > 0 && (n.maxv = r.maxv) : (t.push(r), n = r));
   return t;
 }
-function z(o, e) {
-  return { lineCount: X(j.fromBytesLE(Array.prototype.slice.call(o, e, e + 8), !0)) };
+function G(o, e) {
+  return {
+    lineCount: Y.fromBytesLE(Array.prototype.slice.call(o, e, e + 8), !0).toNumber()
+  };
 }
-function L(o, e) {
+function S(o, e) {
   return o ? o.compareTo(e) > 0 ? e : o : e;
 }
-function ee(o, e = (t) => t) {
+function te(o, e = (t) => t) {
   let t = 0, n = 0;
   const r = [], s = {};
   for (let i = 0; i < o.length; i += 1)
@@ -98,7 +95,7 @@ function ee(o, e = (t) => t) {
     }
   return { refNameToId: s, refIdToName: r };
 }
-class O {
+class H {
   /**
    * @param {filehandle} filehandle
    * @param {function} [renameRefSeqs]
@@ -107,14 +104,14 @@ class O {
     this.filehandle = e, this.renameRefSeq = t;
   }
 }
-const te = 21578050;
-function ne(o, e) {
+const ne = 21578050;
+function re(o, e) {
   return o - o % e;
 }
-function re(o, e) {
+function se(o, e) {
   return o - o % e + e;
 }
-function se(o, e) {
+function ie(o, e) {
   return e -= 1, [
     [0, 0],
     [1 + (o >> 26), 1 + (e >> 26)],
@@ -124,7 +121,7 @@ function se(o, e) {
     [4681 + (o >> 14), 4681 + (e >> 14)]
   ];
 }
-class v extends O {
+class v extends H {
   async lineCount(e, t) {
     var n, r;
     return ((r = (n = (await this.parse(t)).indices[e]) === null || n === void 0 ? void 0 : n.stats) === null || r === void 0 ? void 0 : r.lineCount) || 0;
@@ -132,74 +129,74 @@ class v extends O {
   // fetch and parse the index
   async _parse(e) {
     const t = await this.filehandle.readFile(e);
-    if (t.readUInt32LE(0) !== te)
+    if (t.readUInt32LE(0) !== ne)
       throw new Error("Not a BAI file");
     const n = t.readInt32LE(4), s = ((1 << (5 + 1) * 3) - 1) / 7;
     let i = 8, c;
-    const d = new Array(n);
-    for (let a = 0; a < n; a++) {
-      const l = t.readInt32LE(i);
-      let x;
+    const a = new Array(n);
+    for (let d = 0; d < n; d++) {
+      const f = t.readInt32LE(i);
+      let h;
       i += 4;
-      const h = {};
-      for (let b = 0; b < l; b += 1) {
+      const l = {};
+      for (let b = 0; b < f; b += 1) {
         const u = t.readUInt32LE(i);
         if (i += 4, u === s + 1)
-          i += 4, x = z(t, i + 16), i += 32;
+          i += 4, h = G(t, i + 16), i += 32;
         else {
           if (u > s + 1)
             throw new Error("bai index contains too many bins, please use CSI");
           {
             const g = t.readInt32LE(i);
             i += 4;
-            const p = new Array(g);
-            for (let w = 0; w < g; w++) {
-              const y = E(t, i);
+            const w = new Array(g);
+            for (let _ = 0; _ < g; _++) {
+              const I = E(t, i);
               i += 8;
-              const S = E(t, i);
-              i += 8, c = L(c, y), p[w] = new $(y, S, u);
+              const M = E(t, i);
+              i += 8, c = S(c, I), w[_] = new F(I, M, u);
             }
-            h[u] = p;
+            l[u] = w;
           }
         }
       }
-      const f = t.readInt32LE(i);
+      const x = t.readInt32LE(i);
       i += 4;
-      const m = new Array(f);
-      for (let b = 0; b < f; b++) {
+      const m = new Array(x);
+      for (let b = 0; b < x; b++) {
         const u = E(t, i);
-        i += 8, c = L(c, u), m[b] = u;
+        i += 8, c = S(c, u), m[b] = u;
       }
-      d[a] = { binIndex: h, linearIndex: m, stats: x };
+      a[d] = { binIndex: l, linearIndex: m, stats: h };
     }
     return {
       bai: !0,
       firstDataLine: c,
       maxBlockSize: 65536,
-      indices: d,
+      indices: a,
       refCount: n
     };
   }
   async indexCov(e, t, n, r = {}) {
-    const i = t !== void 0, d = (await this.parse(r)).indices[e];
-    if (!d)
+    const i = t !== void 0, a = (await this.parse(r)).indices[e];
+    if (!a)
       return [];
-    const { linearIndex: a = [], stats: l } = d;
-    if (a.length === 0)
+    const { linearIndex: d = [], stats: f } = a;
+    if (d.length === 0)
       return [];
-    const x = n === void 0 ? (a.length - 1) * 16384 : re(n, 16384), h = t === void 0 ? 0 : ne(t, 16384), f = i ? new Array((x - h) / 16384) : new Array(a.length - 1), m = a[a.length - 1].blockPosition;
-    if (x > (a.length - 1) * 16384)
+    const h = n === void 0 ? (d.length - 1) * 16384 : se(n, 16384), l = t === void 0 ? 0 : re(t, 16384), x = i ? new Array((h - l) / 16384) : new Array(d.length - 1), m = d[d.length - 1].blockPosition;
+    if (h > (d.length - 1) * 16384)
       throw new Error("query outside of range of linear index");
-    let b = a[h / 16384].blockPosition;
-    for (let u = h / 16384, g = 0; u < x / 16384; u++, g++)
-      f[g] = {
-        score: a[u + 1].blockPosition - b,
+    let b = d[l / 16384].blockPosition;
+    for (let u = l / 16384, g = 0; u < h / 16384; u++, g++)
+      x[g] = {
+        score: d[u + 1].blockPosition - b,
         start: u * 16384,
         end: u * 16384 + 16384
-      }, b = a[u + 1].blockPosition;
-    return f.map((u) => ({
+      }, b = d[u + 1].blockPosition;
+    return x.map((u) => ({
       ...u,
-      score: u.score * ((l == null ? void 0 : l.lineCount) || 0) / m
+      score: u.score * ((f == null ? void 0 : f.lineCount) || 0) / m
     }));
   }
   async blocksForRange(e, t, n, r = {}) {
@@ -210,22 +207,22 @@ class v extends O {
     const i = s.indices[e];
     if (!i)
       return [];
-    const c = se(t, n), d = [];
-    for (const [f, m] of c)
-      for (let b = f; b <= m; b++)
+    const c = ie(t, n), a = [];
+    for (const [x, m] of c)
+      for (let b = x; b <= m; b++)
         if (i.binIndex[b]) {
           const u = i.binIndex[b];
           for (const g of u)
-            d.push(g);
+            a.push(new F(g.minv, g.maxv, b));
         }
-    const a = i.linearIndex.length;
-    let l;
-    const x = Math.min(t >> 14, a - 1), h = Math.min(n >> 14, a - 1);
-    for (let f = x; f <= h; ++f) {
-      const m = i.linearIndex[f];
-      m && (!l || m.compareTo(l) < 0) && (l = m);
+    const d = i.linearIndex.length;
+    let f;
+    const h = Math.min(t >> 14, d - 1), l = Math.min(n >> 14, d - 1);
+    for (let x = h; x <= l; ++x) {
+      const m = i.linearIndex[x];
+      m && (!f || m.compareTo(f) < 0) && (f = m);
     }
-    return U(d, l);
+    return z(a, f);
   }
   async parse(e = {}) {
     return this.setupP || (this.setupP = this._parse(e).catch((t) => {
@@ -237,7 +234,7 @@ class v extends O {
     return !!(!((n = (await this.parse(t)).indices[e]) === null || n === void 0) && n.binIndex);
   }
 }
-let T = [
+let B = [
   0,
   1996959894,
   3993919788,
@@ -495,25 +492,25 @@ let T = [
   1510334235,
   755167117
 ];
-typeof Int32Array < "u" && (T = new Int32Array(T));
+typeof Int32Array < "u" && (B = new Int32Array(B));
 const ae = (o, e) => {
   let t = e === 0 ? 0 : ~~e ^ -1;
   for (let n = 0; n < o.length; n++)
-    t = T[(t ^ o[n]) & 255] ^ t >>> 8;
+    t = B[(t ^ o[n]) & 255] ^ t >>> 8;
   return t ^ -1;
-}, M = (o, e) => I.Buffer.from(o, e);
-function ie(o, e) {
-  const t = (n, r) => e(M(n), r) >>> 0;
-  return t.signed = (n, r) => e(M(n), r), t.unsigned = t, t.model = o, t;
+}, N = (o, e) => y.Buffer.from(o, e);
+function oe(o, e) {
+  const t = (n, r) => e(N(n), r) >>> 0;
+  return t.signed = (n, r) => e(N(n), r), t.unsigned = t, t.model = o, t;
 }
-const oe = ie("crc-32", ae), de = 21582659, ce = 38359875;
-function fe(o, e) {
+const ce = oe("crc-32", ae), de = 21582659, fe = 38359875;
+function he(o, e) {
   return o * 2 ** e;
 }
-function F(o, e) {
+function q(o, e) {
   return Math.floor(o / 2 ** e);
 }
-class P extends O {
+class T extends H {
   constructor() {
     super(...arguments), this.maxBinNumber = 0, this.depth = 0, this.minShift = 0;
   }
@@ -532,61 +529,61 @@ class P extends O {
       ref: e.readInt32LE(t + 4),
       start: e.readInt32LE(t + 8),
       end: e.readInt32LE(t + 12)
-    }, c = e.readInt32LE(t + 16), d = c ? String.fromCharCode(c) : "", a = e.readInt32LE(t + 20), l = e.readInt32LE(t + 24);
+    }, c = e.readInt32LE(t + 16), a = c ? String.fromCharCode(c) : "", d = e.readInt32LE(t + 20), f = e.readInt32LE(t + 24);
     return {
       columnNumbers: i,
       coordinateType: r,
       metaValue: c,
-      metaChar: d,
-      skipLines: a,
+      metaChar: a,
+      skipLines: d,
       format: s,
       formatFlags: n,
-      ...ee(e.subarray(t + 28, t + 28 + l), this.renameRefSeq)
+      ...te(e.subarray(t + 28, t + 28 + f), this.renameRefSeq)
     };
   }
   // fetch and parse the index
   async _parse(e) {
-    const t = await this.filehandle.readFile(e), n = await R(t);
+    const t = await this.filehandle.readFile(e), n = await P(t);
     let r;
     if (n.readUInt32LE(0) === de)
       r = 1;
-    else if (n.readUInt32LE(0) === ce)
+    else if (n.readUInt32LE(0) === fe)
       r = 2;
     else
       throw new Error("Not a CSI file");
     this.minShift = n.readInt32LE(4), this.depth = n.readInt32LE(8), this.maxBinNumber = ((1 << (this.depth + 1) * 3) - 1) / 7;
     const s = n.readInt32LE(12), i = s >= 30 ? this.parseAuxData(n, 16) : void 0, c = n.readInt32LE(16 + s);
-    let d = 16 + s + 4, a;
-    const l = new Array(c);
-    for (let x = 0; x < c; x++) {
-      const h = n.readInt32LE(d);
-      d += 4;
-      const f = {};
+    let a = 16 + s + 4, d;
+    const f = new Array(c);
+    for (let h = 0; h < c; h++) {
+      const l = n.readInt32LE(a);
+      a += 4;
+      const x = {};
       let m;
-      for (let b = 0; b < h; b++) {
-        const u = n.readUInt32LE(d);
-        if (d += 4, u > this.maxBinNumber)
-          m = z(n, d + 28), d += 44;
+      for (let b = 0; b < l; b++) {
+        const u = n.readUInt32LE(a);
+        if (a += 4, u > this.maxBinNumber)
+          m = G(n, a + 28), a += 44;
         else {
-          a = L(a, E(n, d)), d += 8;
-          const g = n.readInt32LE(d);
-          d += 4;
-          const p = new Array(g);
-          for (let w = 0; w < g; w += 1) {
-            const y = E(n, d);
-            d += 8;
-            const S = E(n, d);
-            d += 8, a = L(a, y), p[w] = new $(y, S, u);
+          d = S(d, E(n, a)), a += 8;
+          const g = n.readInt32LE(a);
+          a += 4;
+          const w = new Array(g);
+          for (let _ = 0; _ < g; _ += 1) {
+            const I = E(n, a);
+            a += 8;
+            const M = E(n, a);
+            a += 8, d = S(d, I), w[_] = new F(I, M, u);
           }
-          f[u] = p;
+          x[u] = w;
         }
       }
-      l[x] = { binIndex: f, stats: m };
+      f[h] = { binIndex: x, stats: m };
     }
     return {
       csiVersion: r,
-      firstDataLine: a,
-      indices: l,
+      firstDataLine: d,
+      indices: f,
       refCount: c,
       csi: !0,
       maxBlockSize: 65536,
@@ -595,21 +592,21 @@ class P extends O {
   }
   async blocksForRange(e, t, n, r = {}) {
     t < 0 && (t = 0);
-    const s = await this.parse(r), i = s == null ? void 0 : s.indices[e];
+    const i = (await this.parse(r)).indices[e];
     if (!i)
       return [];
     const c = this.reg2bins(t, n);
     if (c.length === 0)
       return [];
-    const d = [];
-    for (const [a, l] of c)
-      for (let x = a; x <= l; x++)
-        if (i.binIndex[x]) {
-          const h = i.binIndex[x];
-          for (const f of h)
-            d.push(f);
+    const a = [];
+    for (const [d, f] of c)
+      for (let h = d; h <= f; h++)
+        if (i.binIndex[h]) {
+          const l = i.binIndex[h];
+          for (const x of l)
+            a.push(x);
         }
-    return U(d, new D(0, 0));
+    return z(a, new O(0, 0));
   }
   /**
    * calculate the list of bins that may overlap with region [beg,end)
@@ -619,11 +616,11 @@ class P extends O {
     e -= 1, e < 1 && (e = 1), t > 2 ** 50 && (t = 2 ** 34), t -= 1;
     let n = 0, r = 0, s = this.minShift + this.depth * 3;
     const i = [];
-    for (; n <= this.depth; s -= 3, r += fe(1, n * 3), n += 1) {
-      const c = r + F(e, s), d = r + F(t, s);
-      if (d - c + i.length > this.maxBinNumber)
+    for (; n <= this.depth; s -= 3, r += he(1, n * 3), n += 1) {
+      const c = r + q(e, s), a = r + q(t, s);
+      if (a - c + i.length > this.maxBinNumber)
         throw new Error(`query ${e}-${t} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`);
-      i.push([c, d]);
+      i.push([c, a]);
     }
     return i;
   }
@@ -637,7 +634,7 @@ class P extends O {
     return !!(!((n = (await this.parse(t)).indices[e]) === null || n === void 0) && n.binIndex);
   }
 }
-const _ = {
+const p = {
   //  the read is paired in sequencing, no matter whether it is mapped in a pair
   BAM_FPAIRED: 1,
   //  the read is mapped in a proper pair
@@ -662,319 +659,273 @@ const _ = {
   BAM_FDUP: 1024,
   //  supplementary alignment
   BAM_FSUPPLEMENTARY: 2048
-}, B = "=ACMGRSVTWYHKDBN".split(""), A = "MIDNSHP=X???????".split("");
-class he {
+}, D = "=ACMGRSVTWYHKDBN".split(""), A = "MIDNSHP=X???????".split("");
+class R {
   constructor(e) {
-    this.data = {}, this._tagList = [], this._allTagsParsed = !1;
-    const { bytes: t, fileOffset: n } = e, { byteArray: r, start: s } = t;
-    this.data = { start: r.readInt32LE(s + 8) }, this.bytes = t, this._id = n, this._refID = r.readInt32LE(s + 4), this.flags = (r.readInt32LE(s + 16) & 4294901760) >> 16;
-  }
-  get(e) {
-    return this[e] ? this.data[e] ? this.data[e] : (this.data[e] = this[e](), this.data[e]) : this._get(e.toLowerCase());
-  }
-  end() {
-    return this.get("start") + this.get("length_on_ref");
-  }
-  seq_id() {
-    return this._refID;
-  }
-  // same as get(), except requires lower-case arguments.  used
-  // internally to save lots of calls to field.toLowerCase()
-  _get(e) {
-    return e in this.data ? this.data[e] : (this.data[e] = this._parseTag(e), this.data[e]);
-  }
-  _tags() {
-    this._parseAllTags();
-    let e = ["seq"];
-    this.isSegmentUnmapped() || e.push("start", "end", "strand", "score", "qual", "MQ", "CIGAR", "length_on_ref", "template_length"), this.isPaired() && e.push("next_segment_position", "pair_orientation"), e = e.concat(this._tagList || []);
-    for (const n of Object.keys(this.data))
-      !n.startsWith("_") && n !== "next_seq_id" && e.push(n);
-    const t = {};
-    return e.filter((n) => {
-      if (n in this.data && this.data[n] === void 0 || n === "CG" || n === "cg")
-        return !1;
-      const r = n.toLowerCase(), s = t[r];
-      return t[r] = !0, !s;
-    });
+    this.bytes = e.bytes, this.fileOffset = e.fileOffset;
   }
-  parent() {
+  get byteArray() {
+    return this.bytes.byteArray;
   }
-  children() {
-    return this.get("subfeatures");
+  get flags() {
+    return (this.byteArray.readInt32LE(this.bytes.start + 16) & 4294901760) >> 16;
   }
-  id() {
-    return this._id;
+  get ref_id() {
+    return this.byteArray.readInt32LE(this.bytes.start + 4);
   }
-  // special parsers
-  /**
-   * Mapping quality score.
-   */
-  mq() {
-    const e = (this.get("_bin_mq_nl") & 65280) >> 8;
-    return e === 255 ? void 0 : e;
+  get start() {
+    return this.byteArray.readInt32LE(this.bytes.start + 8);
   }
-  score() {
-    return this.get("mq");
+  get end() {
+    return this.start + this.length_on_ref;
+  }
+  get id() {
+    return this.fileOffset;
+  }
+  get mq() {
+    const e = (this.bin_mq_nl & 65280) >> 8;
+    return e === 255 ? void 0 : e;
   }
-  qual() {
-    var e;
-    return (e = this.qualRaw()) === null || e === void 0 ? void 0 : e.join(" ");
+  get score() {
+    return this.mq;
   }
-  qualRaw() {
+  get qual() {
     if (this.isSegmentUnmapped())
       return;
-    const { start: e, byteArray: t } = this.bytes, n = e + 36 + this.get("_l_read_name") + this.get("_n_cigar_op") * 4 + this.get("_seq_bytes"), r = this.get("seq_length");
-    return t.subarray(n, n + r);
+    const e = this.b0 + this.read_name_length + this.num_cigar_ops * 4 + this.num_seq_bytes;
+    return this.byteArray.subarray(e, e + this.seq_length);
   }
-  strand() {
+  get strand() {
     return this.isReverseComplemented() ? -1 : 1;
   }
-  multi_segment_next_segment_strand() {
-    if (!this.isMateUnmapped())
-      return this.isMateReverseComplemented() ? -1 : 1;
-  }
-  name() {
-    return this.get("_read_name");
-  }
-  _read_name() {
-    const e = this.get("_l_read_name"), { byteArray: t, start: n } = this.bytes;
-    return t.toString("ascii", n + 36, n + 36 + e - 1);
-  }
-  /**
-   * Get the value of a tag, parsing the tags as far as necessary.
-   * Only called if we have not already parsed that field.
-   */
-  _parseTag(e) {
-    if (this._allTagsParsed)
-      return;
-    const { byteArray: t, start: n } = this.bytes;
-    let r = this._tagOffset || n + 36 + this.get("_l_read_name") + this.get("_n_cigar_op") * 4 + this.get("_seq_bytes") + this.get("seq_length");
-    const s = this.bytes.end;
-    let i;
-    for (; r < s && i !== e; ) {
-      const c = String.fromCharCode(t[r], t[r + 1]);
-      i = c.toLowerCase();
-      const d = String.fromCharCode(t[r + 2]);
-      r += 3;
-      let a;
-      switch (d) {
-        case "A": {
-          a = String.fromCharCode(t[r]), r += 1;
-          break;
-        }
-        case "i": {
-          a = t.readInt32LE(r), r += 4;
-          break;
-        }
-        case "I": {
-          a = t.readUInt32LE(r), r += 4;
-          break;
-        }
-        case "c": {
-          a = t.readInt8(r), r += 1;
-          break;
-        }
-        case "C": {
-          a = t.readUInt8(r), r += 1;
-          break;
-        }
-        case "s": {
-          a = t.readInt16LE(r), r += 2;
-          break;
-        }
-        case "S": {
-          a = t.readUInt16LE(r), r += 2;
-          break;
-        }
-        case "f": {
-          a = t.readFloatLE(r), r += 4;
-          break;
+  get b0() {
+    return this.bytes.start + 36;
+  }
+  get name() {
+    return this.byteArray.toString("ascii", this.b0, this.b0 + this.read_name_length - 1);
+  }
+  get tags() {
+    const { byteArray: e } = this.bytes;
+    let t = this.b0 + this.read_name_length + this.num_cigar_ops * 4 + this.num_seq_bytes + this.seq_length;
+    const n = this.bytes.end, r = {};
+    for (; t < n; ) {
+      const s = String.fromCharCode(e[t], e[t + 1]), i = String.fromCharCode(e[t + 2]);
+      if (t += 3, i === "A")
+        r[s] = String.fromCharCode(e[t]), t += 1;
+      else if (i === "i")
+        r[s] = e.readInt32LE(t), t += 4;
+      else if (i === "I")
+        r[s] = e.readUInt32LE(t), t += 4;
+      else if (i === "c")
+        r[s] = e.readInt8(t), t += 1;
+      else if (i === "C")
+        r[s] = e.readUInt8(t), t += 1;
+      else if (i === "s")
+        r[s] = e.readInt16LE(t), t += 2;
+      else if (i === "S")
+        r[s] = e.readUInt16LE(t), t += 2;
+      else if (i === "f")
+        r[s] = e.readFloatLE(t), t += 4;
+      else if (i === "Z" || i === "H") {
+        const c = [];
+        for (; t <= n; ) {
+          const a = e[t++];
+          if (a !== 0)
+            c.push(String.fromCharCode(a));
+          else
+            break;
         }
-        case "Z":
-        case "H": {
-          for (a = ""; r <= s; ) {
-            const l = t[r++];
-            if (l === 0)
-              break;
-            a += String.fromCharCode(l);
+        r[s] = c.join("");
+      } else if (i === "B") {
+        const c = e[t++], a = String.fromCharCode(c), d = e.readInt32LE(t);
+        if (t += 4, a === "i")
+          if (s === "CG") {
+            const f = [];
+            for (let h = 0; h < d; h++) {
+              const l = e.readInt32LE(t), x = l >> 4, m = A[l & 15];
+              f.push(x + m), t += 4;
+            }
+            r[s] = f.join("");
+          } else {
+            const f = [];
+            for (let h = 0; h < d; h++)
+              f.push(e.readInt32LE(t)), t += 4;
+            r[s] = f;
           }
-          break;
-        }
-        case "B": {
-          a = "";
-          const l = t[r++], x = String.fromCharCode(l), h = t.readInt32LE(r);
-          if (r += 4, x === "i")
-            if (c === "CG")
-              for (let f = 0; f < h; f++) {
-                const m = t.readInt32LE(r), b = m >> 4, u = A[m & 15];
-                a += b + u, r += 4;
-              }
-            else
-              for (let f = 0; f < h; f++)
-                a += t.readInt32LE(r), f + 1 < h && (a += ","), r += 4;
-          if (x === "I")
-            if (c === "CG")
-              for (let f = 0; f < h; f++) {
-                const m = t.readUInt32LE(r), b = m >> 4, u = A[m & 15];
-                a += b + u, r += 4;
-              }
-            else
-              for (let f = 0; f < h; f++)
-                a += t.readUInt32LE(r), f + 1 < h && (a += ","), r += 4;
-          if (x === "s")
-            for (let f = 0; f < h; f++)
-              a += t.readInt16LE(r), f + 1 < h && (a += ","), r += 2;
-          if (x === "S")
-            for (let f = 0; f < h; f++)
-              a += t.readUInt16LE(r), f + 1 < h && (a += ","), r += 2;
-          if (x === "c")
-            for (let f = 0; f < h; f++)
-              a += t.readInt8(r), f + 1 < h && (a += ","), r += 1;
-          if (x === "C")
-            for (let f = 0; f < h; f++)
-              a += t.readUInt8(r), f + 1 < h && (a += ","), r += 1;
-          if (x === "f")
-            for (let f = 0; f < h; f++)
-              a += t.readFloatLE(r), f + 1 < h && (a += ","), r += 4;
-          break;
+        else if (a === "I")
+          if (s === "CG") {
+            const f = [];
+            for (let h = 0; h < d; h++) {
+              const l = e.readUInt32LE(t), x = l >> 4, m = A[l & 15];
+              f.push(x + m), t += 4;
+            }
+            r[s] = f.join("");
+          } else {
+            const f = [];
+            for (let h = 0; h < d; h++)
+              f.push(e.readUInt32LE(t)), t += 4;
+            r[s] = f;
+          }
+        else if (a === "s") {
+          const f = [];
+          for (let h = 0; h < d; h++)
+            f.push(e.readInt16LE(t)), t += 2;
+          r[s] = f;
+        } else if (a === "S") {
+          const f = [];
+          for (let h = 0; h < d; h++)
+            f.push(e.readUInt16LE(t)), t += 2;
+          r[s] = f;
+        } else if (a === "c") {
+          const f = [];
+          for (let h = 0; h < d; h++)
+            f.push(e.readInt8(t)), t += 1;
+          r[s] = f;
+        } else if (a === "C") {
+          const f = [];
+          for (let h = 0; h < d; h++)
+            f.push(e.readUInt8(t)), t += 1;
+          r[s] = f;
+        } else if (a === "f") {
+          const f = [];
+          for (let h = 0; h < d; h++)
+            f.push(e.readFloatLE(t)), t += 4;
+          r[s] = f;
         }
-        default:
-          console.warn(`Unknown BAM tag type '${d}', tags may be incomplete`), a = void 0, r = s;
+      } else {
+        console.error("Unknown BAM tag type", i);
+        break;
       }
-      if (this._tagOffset = r, this._tagList.push(c), i === e)
-        return a;
-      this.data[i] = a;
     }
-    this._allTagsParsed = !0;
-  }
-  _parseAllTags() {
-    this._parseTag("");
-  }
-  _parseCigar(e) {
-    return (
-      //@ts-ignore
-      e.match(/\d+\D/g).map((t) => [/\D/.exec(t)[0].toUpperCase(), Number.parseInt(t, 10)])
-    );
+    return r;
   }
   /**
    * @returns {boolean} true if the read is paired, regardless of whether both
    * segments are mapped
    */
   isPaired() {
-    return !!(this.flags & _.BAM_FPAIRED);
+    return !!(this.flags & p.BAM_FPAIRED);
   }
   /** @returns {boolean} true if the read is paired, and both segments are mapped */
   isProperlyPaired() {
-    return !!(this.flags & _.BAM_FPROPER_PAIR);
+    return !!(this.flags & p.BAM_FPROPER_PAIR);
   }
   /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
   isSegmentUnmapped() {
-    return !!(this.flags & _.BAM_FUNMAP);
+    return !!(this.flags & p.BAM_FUNMAP);
   }
   /** @returns {boolean} true if the read itself is unmapped; conflictive with isProperlyPaired */
   isMateUnmapped() {
-    return !!(this.flags & _.BAM_FMUNMAP);
+    return !!(this.flags & p.BAM_FMUNMAP);
   }
   /** @returns {boolean} true if the read is mapped to the reverse strand */
   isReverseComplemented() {
-    return !!(this.flags & _.BAM_FREVERSE);
+    return !!(this.flags & p.BAM_FREVERSE);
   }
   /** @returns {boolean} true if the mate is mapped to the reverse strand */
   isMateReverseComplemented() {
-    return !!(this.flags & _.BAM_FMREVERSE);
+    return !!(this.flags & p.BAM_FMREVERSE);
   }
   /** @returns {boolean} true if this is read number 1 in a pair */
   isRead1() {
-    return !!(this.flags & _.BAM_FREAD1);
+    return !!(this.flags & p.BAM_FREAD1);
   }
   /** @returns {boolean} true if this is read number 2 in a pair */
   isRead2() {
-    return !!(this.flags & _.BAM_FREAD2);
+    return !!(this.flags & p.BAM_FREAD2);
   }
   /** @returns {boolean} true if this is a secondary alignment */
   isSecondary() {
-    return !!(this.flags & _.BAM_FSECONDARY);
+    return !!(this.flags & p.BAM_FSECONDARY);
   }
   /** @returns {boolean} true if this read has failed QC checks */
   isFailedQc() {
-    return !!(this.flags & _.BAM_FQCFAIL);
+    return !!(this.flags & p.BAM_FQCFAIL);
   }
   /** @returns {boolean} true if the read is an optical or PCR duplicate */
   isDuplicate() {
-    return !!(this.flags & _.BAM_FDUP);
+    return !!(this.flags & p.BAM_FDUP);
   }
   /** @returns {boolean} true if this is a supplementary alignment */
   isSupplementary() {
-    return !!(this.flags & _.BAM_FSUPPLEMENTARY);
+    return !!(this.flags & p.BAM_FSUPPLEMENTARY);
   }
-  cigar() {
+  get cigarAndLength() {
     if (this.isSegmentUnmapped())
-      return;
-    const { byteArray: e, start: t } = this.bytes, n = this.get("_n_cigar_op");
-    let r = t + 36 + this.get("_l_read_name");
-    const s = this.get("seq_length");
-    let i = "", c = 0, d = e.readInt32LE(r), a = d >> 4, l = A[d & 15];
-    if (l === "S" && a === s)
-      return r += 4, d = e.readInt32LE(r), a = d >> 4, l = A[d & 15], l !== "N" && console.warn("CG tag with no N tag"), this.data.length_on_ref = a, this.get("CG");
-    for (let x = 0; x < n; ++x)
-      d = e.readInt32LE(r), a = d >> 4, l = A[d & 15], i += a + l, l !== "H" && l !== "S" && l !== "I" && (c += a), r += 4;
-    return this.data.length_on_ref = c, i;
+      return {
+        length_on_ref: 0,
+        CIGAR: ""
+      };
+    const e = this.num_cigar_ops;
+    let t = this.b0 + this.read_name_length;
+    const n = [];
+    let r = this.byteArray.readInt32LE(t), s = r >> 4, i = A[r & 15];
+    if (i === "S" && s === this.seq_length)
+      return t += 4, r = this.byteArray.readInt32LE(t), s = r >> 4, i = A[r & 15], i !== "N" && console.warn("CG tag with no N tag"), {
+        CIGAR: this.tags.CG,
+        length_on_ref: s
+      };
+    {
+      let c = 0;
+      for (let a = 0; a < e; ++a)
+        r = this.byteArray.readInt32LE(t), s = r >> 4, i = A[r & 15], n.push(s + i), i !== "H" && i !== "S" && i !== "I" && (c += s), t += 4;
+      return {
+        CIGAR: n.join(""),
+        length_on_ref: c
+      };
+    }
   }
-  length_on_ref() {
-    return this.data.length_on_ref ? this.data.length_on_ref : (this.get("cigar"), this.data.length_on_ref);
+  get length_on_ref() {
+    return this.cigarAndLength.length_on_ref;
   }
-  _n_cigar_op() {
-    return this.get("_flag_nc") & 65535;
+  get CIGAR() {
+    return this.cigarAndLength.CIGAR;
   }
-  _l_read_name() {
-    return this.get("_bin_mq_nl") & 255;
+  get num_cigar_ops() {
+    return this.flag_nc & 65535;
   }
-  /**
-   * number of bytes in the sequence field
-   */
-  _seq_bytes() {
-    return this.get("seq_length") + 1 >> 1;
-  }
-  getReadBases() {
-    return this.seq();
-  }
-  seq() {
-    const { byteArray: e, start: t } = this.bytes, n = t + 36 + this.get("_l_read_name") + this.get("_n_cigar_op") * 4, r = this.get("_seq_bytes"), s = this.get("seq_length");
-    let i = "", c = 0;
-    for (let d = 0; d < r; ++d) {
-      const a = e[n + d];
-      i += B[(a & 240) >> 4], c++, c < s && (i += B[a & 15], c++);
+  get read_name_length() {
+    return this.bin_mq_nl & 255;
+  }
+  get num_seq_bytes() {
+    return this.seq_length + 1 >> 1;
+  }
+  get seq() {
+    const { byteArray: e } = this.bytes, t = this.b0 + this.read_name_length + this.num_cigar_ops * 4, n = this.num_seq_bytes, r = this.seq_length, s = [];
+    let i = 0;
+    for (let c = 0; c < n; ++c) {
+      const a = e[t + c];
+      s.push(D[(a & 240) >> 4]), i++, i < r && (s.push(D[a & 15]), i++);
     }
-    return i;
+    return s.join("");
   }
   // adapted from igv.js
-  getPairOrientation() {
-    if (!this.isSegmentUnmapped() && !this.isMateUnmapped() && this._refID === this._next_refid()) {
+  get pair_orientation() {
+    if (!this.isSegmentUnmapped() && !this.isMateUnmapped() && this.ref_id === this.next_refid) {
       const e = this.isReverseComplemented() ? "R" : "F", t = this.isMateReverseComplemented() ? "R" : "F";
       let n = " ", r = " ";
       this.isRead1() ? (n = "1", r = "2") : this.isRead2() && (n = "2", r = "1");
       const s = [];
-      return this.template_length() > 0 ? (s[0] = e, s[1] = n, s[2] = t, s[3] = r) : (s[2] = e, s[3] = n, s[0] = t, s[1] = r), s.join("");
+      return this.template_length > 0 ? (s[0] = e, s[1] = n, s[2] = t, s[3] = r) : (s[2] = e, s[3] = n, s[0] = t, s[1] = r), s.join("");
     }
-    return "";
   }
-  _bin_mq_nl() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 12);
+  get bin_mq_nl() {
+    return this.byteArray.readInt32LE(this.bytes.start + 12);
   }
-  _flag_nc() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 16);
+  get flag_nc() {
+    return this.byteArray.readInt32LE(this.bytes.start + 16);
   }
-  seq_length() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 20);
+  get seq_length() {
+    return this.byteArray.readInt32LE(this.bytes.start + 20);
   }
-  _next_refid() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 24);
+  get next_refid() {
+    return this.byteArray.readInt32LE(this.bytes.start + 24);
   }
-  _next_pos() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 28);
+  get next_pos() {
+    return this.byteArray.readInt32LE(this.bytes.start + 28);
   }
-  template_length() {
-    return this.bytes.byteArray.readInt32LE(this.bytes.start + 32);
+  get template_length() {
+    return this.byteArray.readInt32LE(this.bytes.start + 32);
   }
   toJSON() {
     const e = {};
@@ -983,21 +934,39 @@ class he {
     return e;
   }
 }
-function H(o) {
+function k(o, e) {
+  const t = Object.getOwnPropertyDescriptor(o.prototype, e);
+  if (!t)
+    throw new Error("OH NO, NO PROPERTY DESCRIPTOR");
+  const n = t.get;
+  if (!n)
+    throw new Error("OH NO, NOT A GETTER");
+  Object.defineProperty(o.prototype, e, {
+    get() {
+      const r = n.call(this);
+      return Object.defineProperty(this, e, { value: r }), r;
+    }
+  });
+}
+k(R, "tags");
+k(R, "cigarAndLength");
+k(R, "seq");
+k(R, "qual");
+function j(o) {
   const e = o.split(/\r?\n/), t = [];
   for (const n of e) {
     const [r, ...s] = n.split(/\t/);
     r && t.push({
       tag: r.slice(1),
       data: s.map((i) => {
-        const c = i.indexOf(":"), d = i.slice(0, c), a = i.slice(c + 1);
-        return { tag: d, value: a };
+        const c = i.indexOf(":"), a = i.slice(0, c), d = i.slice(c + 1);
+        return { tag: a, value: d };
       })
     });
   }
   return t;
 }
-const G = 21840194, q = 65536;
+const V = 21840194, $ = 65536;
 async function le(o) {
   let e = [];
   for await (const t of o)
@@ -1019,70 +988,70 @@ class xe {
   }
 }
 class ue {
-  constructor({ bamFilehandle: e, bamPath: t, bamUrl: n, baiPath: r, baiFilehandle: s, baiUrl: i, csiPath: c, csiFilehandle: d, csiUrl: a, htsget: l, yieldThreadTime: x = 100, renameRefSeqs: h = (f) => f }) {
-    if (this.htsget = !1, this.featureCache = new Q({
-      cache: new Y({
+  constructor({ bamFilehandle: e, bamPath: t, bamUrl: n, baiPath: r, baiFilehandle: s, baiUrl: i, csiPath: c, csiFilehandle: a, csiUrl: d, htsget: f, yieldThreadTime: h = 100, renameRefSeqs: l = (x) => x }) {
+    if (this.htsget = !1, this.featureCache = new W({
+      cache: new X({
         maxSize: 50
       }),
-      fill: async (f, m) => {
-        const { chunk: b, opts: u } = f, { data: g, cpositions: p, dpositions: w } = await this._readChunk({
+      fill: async (x, m) => {
+        const { chunk: b, opts: u } = x, { data: g, cpositions: w, dpositions: _ } = await this._readChunk({
           chunk: b,
           opts: { ...u, signal: m }
         });
-        return this.readBamFeatures(g, p, w, b);
+        return this.readBamFeatures(g, w, _, b);
       }
-    }), this.renameRefSeq = h, e)
+    }), this.renameRefSeq = l, e)
       this.bam = e;
     else if (t)
       this.bam = new C(t);
     else if (n)
-      this.bam = new k(n);
-    else if (l)
+      this.bam = new L(n);
+    else if (f)
       this.htsget = !0, this.bam = new xe();
     else
       throw new Error("unable to initialize bam");
-    if (d)
-      this.index = new P({ filehandle: d });
+    if (a)
+      this.index = new T({ filehandle: a });
     else if (c)
-      this.index = new P({ filehandle: new C(c) });
-    else if (a)
-      this.index = new P({ filehandle: new k(a) });
+      this.index = new T({ filehandle: new C(c) });
+    else if (d)
+      this.index = new T({ filehandle: new L(d) });
     else if (s)
       this.index = new v({ filehandle: s });
     else if (r)
       this.index = new v({ filehandle: new C(r) });
     else if (i)
-      this.index = new v({ filehandle: new k(i) });
+      this.index = new v({ filehandle: new L(i) });
     else if (t)
       this.index = new v({ filehandle: new C(`${t}.bai`) });
     else if (n)
-      this.index = new v({ filehandle: new k(`${n}.bai`) });
-    else if (l)
+      this.index = new v({ filehandle: new L(`${n}.bai`) });
+    else if (f)
       this.htsget = !0;
     else
       throw new Error("unable to infer index format");
-    this.yieldThreadTime = x;
+    this.yieldThreadTime = h;
   }
   async getHeaderPre(e) {
-    const t = Z(e);
+    const t = ee(e);
     if (!this.index)
       return;
     const n = await this.index.parse(t), r = n.firstDataLine ? n.firstDataLine.blockPosition + 65535 : void 0;
     let s;
     if (r) {
-      const l = r + q, x = await this.bam.read(I.Buffer.alloc(l), 0, l, 0, t);
-      if (!x.bytesRead)
+      const f = r + $, h = await this.bam.read(y.Buffer.alloc(f), 0, f, 0, t);
+      if (!h.bytesRead)
         throw new Error("Error reading header");
-      s = x.buffer.subarray(0, Math.min(x.bytesRead, r));
+      s = h.buffer.subarray(0, Math.min(h.bytesRead, r));
     } else
       s = await this.bam.readFile(t);
-    const i = await R(s);
-    if (i.readInt32LE(0) !== G)
+    const i = await P(s);
+    if (i.readInt32LE(0) !== V)
       throw new Error("Not a BAM file");
     const c = i.readInt32LE(4);
     this.header = i.toString("utf8", 8, 8 + c);
-    const { chrToIndex: d, indexToChr: a } = await this._readRefSeqs(c + 8, 65535, t);
-    return this.chrToIndex = d, this.indexToChr = a, H(this.header);
+    const { chrToIndex: a, indexToChr: d } = await this._readRefSeqs(c + 8, 65535, t);
+    return this.chrToIndex = a, this.indexToChr = d, j(this.header);
   }
   getHeader(e) {
     return this.headerP || (this.headerP = this.getHeaderPre(e).catch((t) => {
@@ -1097,18 +1066,18 @@ class ue {
   async _readRefSeqs(e, t, n) {
     if (e > t)
       return this._readRefSeqs(e, t * 2, n);
-    const r = t + q, { bytesRead: s, buffer: i } = await this.bam.read(I.Buffer.alloc(r), 0, t, 0, n);
+    const r = t + $, { bytesRead: s, buffer: i } = await this.bam.read(y.Buffer.alloc(r), 0, t, 0, n);
     if (!s)
       throw new Error("Error reading refseqs from header");
-    const c = await R(i.subarray(0, Math.min(s, t))), d = c.readInt32LE(e);
-    let a = e + 4;
-    const l = {}, x = [];
-    for (let h = 0; h < d; h += 1) {
-      const f = c.readInt32LE(a), m = this.renameRefSeq(c.toString("utf8", a + 4, a + 4 + f - 1)), b = c.readInt32LE(a + f + 4);
-      if (l[m] = h, x.push({ refName: m, length: b }), a = a + 8 + f, a > c.length)
+    const c = await P(i.subarray(0, Math.min(s, t))), a = c.readInt32LE(e);
+    let d = e + 4;
+    const f = {}, h = [];
+    for (let l = 0; l < a; l += 1) {
+      const x = c.readInt32LE(d), m = this.renameRefSeq(c.toString("utf8", d + 4, d + 4 + x - 1)), b = c.readInt32LE(d + x + 4);
+      if (f[m] = l, h.push({ refName: m, length: b }), d = d + 8 + x, d > c.length)
         return console.warn(`BAM header is very big.  Re-fetching ${t} bytes.`), this._readRefSeqs(e, t * 2, n);
     }
-    return { chrToIndex: l, indexToChr: x };
+    return { chrToIndex: f, indexToChr: h };
   }
   async getRecordsForRange(e, t, n, r) {
     return le(this.streamRecordsForRange(e, t, n, r));
@@ -1126,76 +1095,76 @@ class ue {
   }
   async *_fetchChunkFeatures(e, t, n, r, s = {}) {
     const { viewAsPairs: i } = s, c = [];
-    let d = !1;
-    for (const a of e) {
-      const l = await this.featureCache.get(a.toString(), { chunk: a, opts: s }, s.signal), x = [];
-      for (const h of l)
-        if (h.seq_id() === t)
-          if (h.get("start") >= r) {
-            d = !0;
+    let a = !1;
+    for (const d of e) {
+      const f = await this.featureCache.get(d.toString(), { chunk: d, opts: s }, s.signal), h = [];
+      for (const l of f)
+        if (l.ref_id === t)
+          if (l.start >= r) {
+            a = !0;
             break;
-          } else h.get("end") >= n && x.push(h);
-      if (c.push(x), yield x, d)
+          } else l.end >= n && h.push(l);
+      if (c.push(h), yield h, a)
         break;
     }
-    J(s.signal), i && (yield this.fetchPairs(t, c, s));
+    K(s.signal), i && (yield this.fetchPairs(t, c, s));
   }
   async fetchPairs(e, t, n) {
     const { pairAcrossChr: r, maxInsertSize: s = 2e5 } = n, i = {}, c = {};
-    t.map((h) => {
-      const f = {};
-      for (const m of h) {
-        const b = m.name(), u = m.id();
-        f[b] || (f[b] = 0), f[b]++, c[u] = 1;
+    t.map((l) => {
+      const x = {};
+      for (const m of l) {
+        const b = m.name, u = m.id;
+        x[b] || (x[b] = 0), x[b]++, c[u] = 1;
       }
-      for (const [m, b] of Object.entries(f))
+      for (const [m, b] of Object.entries(x))
         b === 1 && (i[m] = !0);
     });
-    const d = [];
-    t.map((h) => {
-      for (const f of h) {
-        const m = f.name(), b = f.get("start"), u = f._next_pos(), g = f._next_refid();
-        this.index && i[m] && (r || g === e && Math.abs(b - u) < s) && d.push(this.index.blocksForRange(g, u, u + 1, n));
+    const a = [];
+    t.map((l) => {
+      for (const x of l) {
+        const m = x.name, b = x.start, u = x.next_pos, g = x.next_refid;
+        this.index && i[m] && (r || g === e && Math.abs(b - u) < s) && a.push(this.index.blocksForRange(g, u, u + 1, n));
       }
     });
-    const a = /* @__PURE__ */ new Map(), l = await Promise.all(d);
-    for (const h of l.flat())
-      a.has(h.toString()) || a.set(h.toString(), h);
-    return (await Promise.all([...a.values()].map(async (h) => {
-      const { data: f, cpositions: m, dpositions: b, chunk: u } = await this._readChunk({
-        chunk: h,
+    const d = /* @__PURE__ */ new Map(), f = await Promise.all(a);
+    for (const l of f.flat())
+      d.has(l.toString()) || d.set(l.toString(), l);
+    return (await Promise.all([...d.values()].map(async (l) => {
+      const { data: x, cpositions: m, dpositions: b, chunk: u } = await this._readChunk({
+        chunk: l,
         opts: n
       }), g = [];
-      for (const p of await this.readBamFeatures(f, m, b, u))
-        i[p.get("name")] && !c[p.id()] && g.push(p);
+      for (const w of await this.readBamFeatures(x, m, b, u))
+        i[w.name] && !c[w.id] && g.push(w);
       return g;
     }))).flat();
   }
   async _readRegion(e, t, n = {}) {
-    const { bytesRead: r, buffer: s } = await this.bam.read(I.Buffer.alloc(t), 0, t, e, n);
+    const { bytesRead: r, buffer: s } = await this.bam.read(y.Buffer.alloc(t), 0, t, e, n);
     return s.subarray(0, Math.min(r, t));
   }
   async _readChunk({ chunk: e, opts: t }) {
-    const n = await this._readRegion(e.minv.blockPosition, e.fetchedSize(), t), { buffer: r, cpositions: s, dpositions: i } = await V(n, e);
+    const n = await this._readRegion(e.minv.blockPosition, e.fetchedSize(), t), { buffer: r, cpositions: s, dpositions: i } = await Q(n, e);
     return { data: r, cpositions: s, dpositions: i, chunk: e };
   }
   async readBamFeatures(e, t, n, r) {
     let s = 0;
     const i = [];
-    let c = 0, d = +Date.now();
+    let c = 0, a = +Date.now();
     for (; s + 4 < e.length; ) {
-      const a = e.readInt32LE(s), l = s + 4 + a - 1;
+      const d = e.readInt32LE(s), f = s + 4 + d - 1;
       if (n) {
         for (; s + r.minv.dataPosition >= n[c++]; )
           ;
         c--;
       }
-      if (l < e.length) {
-        const x = new he({
+      if (f < e.length) {
+        const h = new R({
           bytes: {
             byteArray: e,
             start: s,
-            end: l
+            end: f
           },
           // the below results in an automatically calculated file-offset based
           // ID if the info for that is available, otherwise crc32 of the
@@ -1219,12 +1188,13 @@ class ue {
           // realistically happen
           fileOffset: t.length > 0 ? t[c] * 256 + (s - n[c]) + r.minv.dataPosition + 1 : (
             // must be slice, not subarray for buffer polyfill on web
-            oe.signed(e.slice(s, l))
+            // eslint-disable-next-line @typescript-eslint/no-deprecated
+            ce.signed(e.slice(s, f))
           )
         });
-        i.push(x), this.yieldThreadTime && +Date.now() - d > this.yieldThreadTime && (await W(1), d = +Date.now());
+        i.push(h), this.yieldThreadTime && +Date.now() - a > this.yieldThreadTime && (await J(1), a = +Date.now());
       }
-      s = l + 1;
+      s = f + 1;
     }
     return i;
   }
@@ -1255,41 +1225,41 @@ class ue {
     return i === void 0 ? [] : this.index.blocksForRange(i, t, n, r);
   }
 }
-async function N(o, e) {
+async function U(o, e) {
   const t = await Promise.all(o.map(async (n) => {
     const { url: r, headers: s } = n;
     if (r.startsWith("data:"))
-      return I.Buffer.from(r.split(",")[1], "base64");
+      return y.Buffer.from(r.split(",")[1], "base64");
     {
-      const { referer: i, ...c } = s, d = await fetch(r, {
+      const { referer: i, ...c } = s, a = await fetch(r, {
         ...e,
         headers: { ...e == null ? void 0 : e.headers, ...c }
       });
-      if (!d.ok)
-        throw new Error(`HTTP ${d.status} fetching ${r}: ${await d.text()}`);
-      return I.Buffer.from(await d.arrayBuffer());
+      if (!a.ok)
+        throw new Error(`HTTP ${a.status} fetching ${r}: ${await a.text()}`);
+      return y.Buffer.from(await a.arrayBuffer());
     }
   }));
-  return I.Buffer.concat(await Promise.all(t.map((n) => R(n))));
+  return y.Buffer.concat(await Promise.all(t.map((n) => P(n))));
 }
-class we extends ue {
+class _e extends ue {
   constructor(e) {
     super({ htsget: !0 }), this.baseUrl = e.baseUrl, this.trackId = e.trackId;
   }
   async *streamRecordsForRange(e, t, n, r) {
     var s;
-    const c = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${t}&end=${n}&format=BAM`, d = (s = this.chrToIndex) === null || s === void 0 ? void 0 : s[e];
-    if (d === void 0)
+    const c = `${`${this.baseUrl}/${this.trackId}`}?referenceName=${e}&start=${t}&end=${n}&format=BAM`, a = (s = this.chrToIndex) === null || s === void 0 ? void 0 : s[e];
+    if (a === void 0)
       yield [];
     else {
-      const a = await fetch(c, { ...r });
-      if (!a.ok)
-        throw new Error(`HTTP ${a.status} fetching ${c}: ${await a.text()}`);
-      const l = await a.json(), x = await N(l.htsget.urls.slice(1), r);
+      const d = await fetch(c, { ...r });
+      if (!d.ok)
+        throw new Error(`HTTP ${d.status} fetching ${c}: ${await d.text()}`);
+      const f = await d.json(), h = await U(f.htsget.urls.slice(1), r);
       yield* this._fetchChunkFeatures([
         // fake stuff to pretend to be a Chunk
         {
-          buffer: x,
+          buffer: h,
           _fetchedSize: void 0,
           bin: 0,
           compareTo() {
@@ -1315,7 +1285,7 @@ class we extends ue {
             return `${e}_${t}_${n}`;
           }
         }
-      ], d, t, n, r);
+      ], a, t, n, r);
     }
   }
   async _readChunk({ chunk: e }) {
@@ -1327,23 +1297,23 @@ class we extends ue {
     const t = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`, n = await fetch(t, e);
     if (!n.ok)
       throw new Error(`HTTP ${n.status} fetching ${t}: ${await n.text()}`);
-    const r = await n.json(), s = await N(r.htsget.urls, e);
-    if (s.readInt32LE(0) !== G)
+    const r = await n.json(), s = await U(r.htsget.urls, e);
+    if (s.readInt32LE(0) !== V)
       throw new Error("Not a BAM file");
-    const i = s.readInt32LE(4), c = s.toString("utf8", 8, 8 + i), d = H(c), a = [], l = {}, x = d.filter((h) => h.tag === "SQ");
-    for (const [h, f] of x.entries()) {
+    const i = s.readInt32LE(4), c = s.toString("utf8", 8, 8 + i), a = j(c), d = [], f = {}, h = a.filter((l) => l.tag === "SQ");
+    for (const [l, x] of h.entries()) {
       let m = "", b = 0;
-      for (const u of f.data)
+      for (const u of x.data)
         u.tag === "SN" ? m = u.value : u.tag === "LN" && (b = +u.value);
-      l[m] = h, a[h] = { refName: m, length: b };
+      f[m] = l, d[l] = { refName: m, length: b };
     }
-    return this.chrToIndex = l, this.indexToChr = a, d;
+    return this.chrToIndex = f, this.indexToChr = d, a;
   }
 }
 export {
   v as BAI,
   ue as BamFile,
-  he as BamRecord,
-  P as CSI,
-  we as HtsgetFile
+  R as BamRecord,
+  T as CSI,
+  _e as HtsgetFile
 };